Use of an inducible site-specific recombinase to probe the structure of protein-DNA complexes involved in F plasmid partition in Escherichia coli.

The induced expression of a tightly regulated site-specific recombinase is shown to efficiently form intracellular DNA rings of well-defined nucleotide sequences in Escherichia coli. To provide information on the organization of an intracellular protein-DNA complex, the linking number distributions of excised DNA rings containing cognate binding sites for the protein can be measured after their isolation. Application of this approach to the partition system of the E. coli F plasmid suggests that the SopB protein and the sopC locus, the latter being composed of 12 tandemly joined imperfect repeats of a 43 base-pair motif, form a complex in which the DNA is wrapped right-handedly around a multimeric protein core; the presence of a single copy of a 43 base-pair motif on a DNA appears to be sufficient to nucleate the formation of this nucleoprotein complex.